# HG changeset patch
# User jfb
# Date 1540923924 14400
# Node ID 81da7e8c5ad140c2d0e898a09c09528afa361a27
# Parent  29da7509ed5498e3f7cb15b7a5845e471ecab1b4
Uploaded

diff -r 29da7509ed54 -r 81da7e8c5ad1 blosum4galaxy/Blosum.xml
--- a/blosum4galaxy/Blosum.xml	Mon Oct 29 16:38:58 2018 -0400
+++ b/blosum4galaxy/Blosum.xml	Tue Oct 30 14:25:24 2018 -0400
@@ -4,13 +4,13 @@
        <requirement type="package">openjdk</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[        
-        java -Djava.awt.headless=true -jar '$__tool_directory__/blosum2.jar'
+        java -Djava.awt.headless=true -jar '$__tool_directory__/blosum2.jar' '$INPUT' output.csv
     ]]></command>
     <inputs>
-        <param format="csv" name="INPUT.csv" type="data" label="Peptide Sequences"/>
+        <param format="csv" name="INPUT" type="data" label="Peptide Sequences"/>
     </inputs>      
     <outputs>
-        <data format="csv" name="BlosumOutput.csv" from_work_dir="BlosumOutput.csv" label="BlosumOutput.csv"/>
+        <data format="csv" name="BlosumOutput.csv" from_work_dir="output.csv" label="BlosumOutput.csv"/>
     </outputs>
     <tests>
         <test>